Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2021 Jul 16;12:4344. doi: 10.1038/s41467-021-24641-4

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 4 — a Significant (q < 0.1; FitHiChIP) H3K4me3 HiChIP interactions identified in WT mESC, Eed^−/− mESC and Tamoxifen-treated Ring1a^−/−Ring1b^fl/fl mESC were plotted according to their loop size. Mid-range (300kb-1mb) loops are significantly reduced (FC = −5.70, p = 0.026; two-sided Wilcoxon test) in Tamoxifen-treated Ring1a^−/−Ring1b^fl/fl mESC compared to WT. PET = paired-end tags. b Significant (mESC H3K27me3 HiChIP data; p < 0.01; FitHiChIP) interactions between distal PEs (>10 kb from TSS) and bivalent promoters (n = 526) were visualized as pileup plots using H3K4me3 HiChIP data generated in WT, Eed^−/− and Tamoxifen-treated Ring1a^−/−Ring1b^fl/fl mESC. HiChIP interaction matrices were coverage-normalized (unbalanced). c H3K4me3 HiChIP in WT, Eed^−/− mESC, and Tamoxifen-treated Ring1a^−/−Ring1b^fl/fl mESC around the Sox1 locus. d Significant (mESC H3K27me3 HiChIP data; p < 0.01; FitHiChIP) interactions between distal PEs (>10 kb from TSS) and bivalent promoters (left panel; n = 526) or between PcG domains (right panel; n = 411) were visualized as pileup plots using Hi-C data generated in the following mESC lines expressing Tir1 and treated with Auxin⁵²: WT mESC (Tir1 Aux), Ring1a^−/−Ring1b^DEG/DEG mESC (i.e. RING1A/B-depleted cells; Ring1b Aux) and Rad21/Scc1^DEG/DEG mESC (i.e. Cohesin depleted cells; Scc1 Aux). Hi-C interaction matrices were KR-balanced (balanced). e Significant (mESC H3K27me3 HiChIP data; p < 0.01; FitHiChIP) interactions between distal PEs (>10 kb from TSS) and bivalent promoters (n = 526) were visualized as pileup plots using Hi-C data generated in the epiblast from WT and Kmt2b/Mll2^−/− E6.5 mouse embryos⁵¹. Hi-C interaction matrices were KR-balanced (balanced). f Significant (mESC H3K27me3 HiChIP data; p < 0.01; FitHiChIP) interactions between distal PEs (>10 kb from TSS) and bivalent promoters (n = 526) were visualized as pileup plots using Hi-C data generated in CTCF-Degron mESC lines⁵³ that were either untreated (CTCF untreated), treated with Auxin for two days (CTCF Aux (2 days)) or treated with Auxin and then washed off (CTCF Aux (washoff)). Interaction matrices were KR-balanced (balanced). In (b, d–f), HiChIP or Hi-C pairwise interactions are shown 250 kb up- and downstream of each PE and bivalent promoter pair. The numbers in the upper left corners correspond to “loopiness” values (center intensity normalized to the intensity in the corners).